In the ledger CDDL we represent the certificates as groups, where the first element of the group is a fixed integer which acts as a tag. Here's what the CDDL looks like:

certificate = 
  [  stake_registration
  // stake_deregistration
  // stake_delegation
  <...>
  ]

stake_registration = (0, stake_credential)

stake_deregistration = (1, stake_credential)

stake_delegation = (2, stake_credential, pool_keyhash)

<...>

I'm not sure how to solve this in the general case, probably there needs to be some complicated procedure that analyzes each of these choices to find a subterm that uniquely determines which choice is the right one. In our usecase however it should be pretty simple to add a heuristic that can handle cases where the first element of each of these groups is a unique integer.